We attempt to reproduce and efficiently implement in MATLAB publicly available methods of Affymetrix MAS 5 and GCOS 1.2 software that perform single-array and comparison analysis for Affymetrix data given by CEL and CDF files and create corresponding CHP data structures:

1. CHP data structure is constructed based on given CEL and CDF files. Detection p-values and Signals are computed and Detection Calls are assigned. Please run the demo provided.

2. CHP comparison analysis data structure is constructed based on two given CEL files: the baseline and the experiment. Change p-values and Signal Log Ratios are computed and Change Calls are assigned. Please run the demo provided.

3. affyCdfCel2chp is a vectorized version of MATLAB Bioinformatics toolbox function "probesetvalues" that efficiently reads Affymetrix data from CDF and CEL structures.

HELP NEEDED:
1. In absolute analysis, we obtain detection detection calls consistent with those from Affymetrix GCOS 1.2 software, but more accurate results for Detection p-values and Signal values are still desirable.

2. In our preliminary tests for comparative analysis, change calls coincide with those computed by GCOS 1.2, but more accurate results are desirable for Change p-values and Signal Log Ratios.

We would appreciate any suggestions, but we especially need help with specific details of the algorithms used in Affymetrix MAS 5 and GCOS 1.2 software highlighted above.